Multikingdom characterization of gut microbiota in patients with rheumatoid arthritis and rheumatoid arthritis‐associated interstitial lung disease

作者：Yida Xing, Yiping Liu, Shanshan Sha, Yue Zhang, Yuemeng Dou, Changyan Liu, Mingxi Xu, Lin Zhao, Jingdan Wang, Yan Wang, Xiaochi Ma, Qiulong Yan, Xiaodan Kong · 发表于：Journal of Medical Virology · 年份：2024 · DOI：10.1002/jmv.29781 · 被引用次数：29 · 研究领域：Mycobacterium research and diagnosis、Gut microbiota and health、Plant and Fungal Interactions Research

Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) is a serious and common extra-articular disease manifestation. Patients with RA-ILD experience reduced bacterial diversity and gut bacteriome alterations. However, the gut mycobiome and virome in these patients have been largely neglected. In this study, we performed whole-metagenome shotgun sequencing on fecal samples from 30 patients with RA-ILD, and 30 with RA-non-ILD, and 40 matched healthy controls. The gut bacteriome and mycobiome were explored using a reference-based approach, while the gut virome was profiled based on a nonredundant viral operational taxonomic unit (vOTU) catalog. The results revealed significant alterations in the gut microbiomes of both RA-ILD and RA-non-ILD groups compared with healthy controls. These alterations encompassed changes in the relative abundances of 351 bacterial species, 65 fungal species, and 4,367 vOTUs. Bacteria such as Bifidobacterium longum, Dorea formicigenerans, and Collinsella aerofaciens were enriched in both patient groups. Ruminococcus gnavus (RA-ILD), Gemmiger formicilis, and Ruminococcus bromii (RA-non-ILD) were uniquely enriched. Conversely, Faecalibacterium prausnitzii, Bacteroides spp., and Roseburia inulinivorans showed depletion in both patient groups. Mycobiome analysis revealed depletion of certain fungi, including Saccharomyces cerevisiae and Candida albicans, in patients with RA compared with healthy subjects. Notably, gut virome alterations were ...